Internet fraud. How is it possible?!

Later that day I entered new credit card number with the reader numbers in iTunes, After I did that I received messages about checking the card from itunes.

'reader numbers' ? And received messages how/where ?

can the application be infected with a virus?

Is the phone jailbroken ? I'm not aware of any viruses that affect non-jailbroken devices, and you presumably downloaded the app from the App Store anyway, not a hacked version. And unless you entered the card's details in the app it wouldn't have access to your payment method.

could there be a risk when you enter the card data on itunes?

If you used your computer and you had, for example, a key logger on the computer when you entered the card's details it's possible. iTunes doesn't store all of the card's details e.g. the security code isn't stored, so even if the iTunes account was hacked the full card's details can't be accessed.

as the card is very new and itunes was the only service where I have entered this card

You haven't used the card anywhere else e.g. not in an actual shop ?

you know any Apple email addresses where I can write about my problem?

If you have proof about how the card's details were taken : http://www.apple.com/support/itunes/ww (click on your country's flag, the country where you live, and which is therefore the country on the account ; click on Contact Support towards the top right ; click on Get Help under 'Talk To Us’)

Contact the card issuer, let them deal with it

Had you used the card in an actual shop ?

You hadn't used the card anywhere else, you hadn't used to pay for anything in a shop ?

Apps don't have access to anything about your account unless you enter those details directly in them, and if someone knew your iTunes account's password they wouldn't be able to get the full card's details (they would only see the last 4 digits of the card).